scholarly journals 8-Bit Adder and Subtractor with Domain Label Based on DNA Strand Displacement

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2989 ◽  
Author(s):  
Weixuan Han ◽  
Changjun Zhou
Keyword(s):  
Dna Computing ◽  
Logic Gates ◽  
Logic Circuits ◽  
Calculation Model ◽  
Strand Displacement ◽  
High Concentration ◽  
Low Concentration ◽  
Molecular Logic ◽  
Dna Strand Displacement ◽  
Dna Strand

DNA strand displacement, which plays a fundamental role in DNA computing, has been widely applied to many biological computing problems, including biological logic circuits. However, there are many biological cascade logic circuits with domain labels based on DNA strand displacement that have not yet been designed. Thus, in this paper, cascade 8-bit adder/subtractor with a domain label is designed based on DNA strand displacement; domain t and domain f represent signal 1 and signal 0, respectively, instead of domain t and domain f are applied to representing signal 1 and signal 0 respectively instead of high concentration and low concentration high concentration and low concentration. Basic logic gates, an amplification gate, a fan-out gate and a reporter gate are correspondingly reconstructed as domain label gates. The simulation results of Visual DSD show the feasibility and accuracy of the logic calculation model of the adder/subtractor designed in this paper. It is a useful exploration that may expand the application of the molecular logic circuit.

Molecular Logic Gates Based on Localized DNA Strand Displacement

2016 ◽  
Vol 13 (6) ◽  
pp. 3948-3952 ◽  
Author(s):  
Yanfeng Wang ◽  
Wenwen Zhang ◽  
Xing Li ◽  
Guangzhao Cui
Keyword(s):  
Logic Gates ◽  
Strand Displacement ◽  
Molecular Logic ◽  
Molecular Logic Gates ◽  
Dna Strand Displacement ◽  
Dna Strand

Research of Molecule Logic Circuit Based on DNA Strand Displacement Reaction

2016 ◽  
Vol 13 (10) ◽  
pp. 7684-7691 ◽  
Author(s):  
Zicheng Wang ◽  
Zijie Cai ◽  
Zhonghua Sun ◽  
Jian Ai ◽  
Yanfeng Wang ◽  
...  
Keyword(s):  
Logic Circuits ◽  
Logic Circuit ◽  
The Other ◽  
Strand Displacement ◽  
Molecular Logic ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Gold Nanoprobe ◽  
Decoder Circuit ◽  
Strand Displacement Reaction

Because of its outstanding advantages, DNA strand displacement (DSD) reaction has been widely used for signals processing and molecular logic circuit constructing. Two digital logic circuits are constructed in this paper. One is the encoder circuit with four inputs and two outputs, and the other is the decoder circuit with two inputs and four outputs. Of particular interest to us is the multicolor fluorescent gold nanoprobe detection part, where a gold nanoparticle is modified with multicolor fluorophores which exploits the ultrahigh quenching ability of gold nanoparticles (AuNPs). Finally, the circuits can be programmed and simulated with the software Visual DSD. The simulated results based on DSD show that the molecular circuits constructed in this paper is reliable and effective, which has wide prospects in logical circuits and nano-electronics study.

Molecular Logic Gate Based on DNA Strand Displacement Reaction

2021 ◽  
Vol 16 (6) ◽  
pp. 974-977
Author(s):  
Jingjing Ma
Keyword(s):  
Logic Gate ◽  
Logic Gates ◽  
Displacement Reaction ◽  
Strand Displacement ◽  
Molecular Logic ◽  
Molecular Logic Gates ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Biochemical Experiment ◽  
Strand Displacement Reaction

In this paper, I construct an XOR logic gate based on DNA strand displacement reaction, and verify our design through corresponding biochemical experiment. I designed several different DNA strands. Based on two basic DNA strand displacement reaction mechanisms, by adding different input strands and taking the signal of FAM fluorescent group as the output, the XOR logic gate is realized. The result shows that DNA strand displacement technology has important application value in DNA computing, especially in the construction of DNA molecular logic gates.

Development of DNA computing and information processing based on DNA-strand displacement

2015 ◽  
Vol 58 (10) ◽  
pp. 1515-1523 ◽  
Author(s):  
Yafei Dong ◽  
Chen Dong ◽  
Fei Wan ◽  
Jing Yang ◽  
Cheng Zhang
Keyword(s):  
Information Processing ◽  
Dna Computing ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand

Pattern Recognition of 2 × 2 Matrices Based on DNA Strand Displacement

2019 ◽  
Vol 11 (10) ◽  
pp. 1357-1365
Author(s):  
Yanfeng Wang ◽  
Aolong LV ◽  
Chun Huang ◽  
Junwei Sun
Keyword(s):  
Pattern Recognition ◽  
Large Scale ◽  
Logic Circuits ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Complex Circuits ◽  
Dna Strand ◽  
Simple Logic

Biochemical circuits have been transformed from simple logic circuits to large-scale complex circuits, benefitting from the maturity of DNA strand displacement technology. Pattern recognition is a process of analyzing perceptual signals and identifying and interpreting objects. In this study, pattern recognition of 2 × 2 matrices based on DNA strand displacement was designed, including dual-rail circuits and seesaw circuits. The effective results were obtained by simulation in Visual DSD software, simultaneously, the pattern recognition and DNA strand displacement technology were perfectly combined.

scholarly journals A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Xin Li ◽  
Xun Wang ◽  
Tao Song ◽  
Wei Lu ◽  
Zhihua Chen ◽  
...  
Keyword(s):  
Reaction Time ◽  
Computational Method ◽  
Ion Concentration ◽  
Strand Displacement ◽  
High Concentration ◽  
Low Leakage ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Structure Reporting ◽  
Dna Strand

DNA strand displacement technique is widely used in DNA programming, DNA biosensors, and gene analysis. In DNA strand displacement, leaky reactions can cause DNA signals decay and detecting DNA signals fails. The mostly used method to avoid leakage is cleaning up after upstream leaky reactions, and it remains a challenge to develop reliable DNA strand displacement technique with low leakage. In this work, we address the challenge by experimentally evaluating the basic factors, including reaction time, ratio of reactants, and ion concentration to the leakage in DNA strand displacement. Specifically, fluorescent probes and a hairpin structure reporting DNA strand are designed to detect the output of DNA strand displacement, and thus can evaluate the leakage of DNA strand displacement reactions with different reaction time, ratios of reactants, and ion concentrations. From the obtained data, mathematical models for evaluating leakage are achieved by curve derivation. As a result, it is obtained that long time incubation, high concentration of fuel strand, and inappropriate amount of ion concentration can weaken leaky reactions. This contributes to a method to set proper reaction conditions to reduce leakage in DNA strand displacement.

scholarly journals A programming language for composable DNA circuits

2009 ◽  
Vol 6 (suppl_4) ◽  
Author(s):  
Andrew Phillips ◽  
Luca Cardelli
Keyword(s):  
Programming Language ◽  
Large Scale ◽  
Implementation Strategies ◽  
Logic Circuits ◽  
Arbitrary System ◽  
Strand Displacement ◽  
Dna Computation ◽  
Simulation Tools ◽  
Dna Strand Displacement ◽  
Dna Strand

Recently, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Examples include digital logic circuits and catalytic signal amplification circuits that function as efficient molecular detectors. As new paradigms for DNA computation emerge, the development of corresponding languages and tools for these paradigms will help to facilitate the design of DNA circuits and their automatic compilation to nucleotide sequences. We present a programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism. The language includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure. The language is used to model and simulate a variety of circuits, including an entropy-driven catalytic gate, a simple gate motif for synthesizing large-scale circuits and a scheme for implementing an arbitrary system of chemical reactions. The language is a first step towards the design of modelling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing.

scholarly journals Abstractions for DNA circuit design

2011 ◽  
Vol 9 (68) ◽  
pp. 470-486 ◽  
Author(s):  
Matthew R. Lakin ◽  
Simon Youssef ◽  
Luca Cardelli ◽  
Andrew Phillips
Keyword(s):  
Reaction Kinetics ◽  
Computational Cost ◽  
Logic Gates ◽  
Strand Displacement ◽  
Levels Of Detail ◽  
Molecular Detail ◽  
Dna Strand Displacement ◽  
Displacement System ◽  
Dna Strand ◽  
High Level

DNA strand displacement techniques have been used to implement a broad range of information processing devices, from logic gates, to chemical reaction networks, to architectures for universal computation. Strand displacement techniques enable computational devices to be implemented in DNA without the need for additional components, allowing computation to be programmed solely in terms of nucleotide sequences. A major challenge in the design of strand displacement devices has been to enable rapid analysis of high-level designs while also supporting detailed simulations that include known forms of interference. Another challenge has been to design devices capable of sustaining precise reaction kinetics over long periods, without relying on complex experimental equipment to continually replenish depleted species over time. In this paper, we present a programming language for designing DNA strand displacement devices, which supports progressively increasing levels of molecular detail. The language allows device designs to be programmed using a common syntax and then analysed at varying levels of detail, with or without interference, without needing to modify the program. This allows a trade-off to be made between the level of molecular detail and the computational cost of analysis. We use the language to design a buffered architecture for DNA devices, capable of maintaining precise reaction kinetics for a potentially unbounded period. We test the effectiveness of buffered gates to support long-running computation by designing a DNA strand displacement system capable of sustained oscillations.

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